Schema Reference

This page provides the complete OpenAPI schema for the SCIENTRY API.

API Endpoints

Below is a comprehensive list of all API endpoints, grouped by resource/tag. Each entry shows the HTTP method, path, and a short summary.

Auth

Method	Path	Summary
POST	/auth/login	User login
POST	/auth/logout	User logout

Users

Method	Path	Summary
GET	/users	List all users
GET	/users/{name}	Get user by name
GET	/users/{name}/projects	Get projects for a user

Stats & Lookup

Method	Path	Summary
GET	/lookup	Global lookup
GET	/records/stats/{field}	Get stats for a record field
GET	/links/stats/{field}	Get stats for a link field
GET	/projects/{project_id}/models/{model_name}/stats/{field}	Get stats for a model field
GET	/projects/{project_id}/{model}/stats/{field}	Get stats for a model in a project

Files

Method	Path	Summary
GET	/files/{hash}/download	Download file by hash
GET	/projects/{project_id}/models/{model_name}/files/{type}/download	Download model files by type

Audit

Method	Path	Summary
GET	/audit-logs	Get all audit logs
GET	/projects/{project_id}/audit-logs	Get audit logs for a project
GET	/audit-logs/{document_type}/{document_id}	Get audit logs for a document

Projects

Method	Path	Summary
GET	/projects	List all projects
POST	/projects	Create a new project
GET	/projects/{project_id}	Get project by ID
PUT	/projects/{project_id}	Update project by ID
DELETE	/projects/{project_id}	Delete project by ID
POST	/projects/{project_id}/archive	Archive a project
POST	/projects/{project_id}/unarchive	Unarchive a project
GET	/projects/{project_id}/schema	Get project schema
GET	/projects/{project_id}/lookup	Lookup project data

Models

Method	Path	Summary
GET	/models	List all models
POST	/models	Create a new model
GET	/projects/{project_id}/models	List models for a project
GET	/projects/{project_id}/models/{model_name}	Get model by name in project
PUT	/projects/{project_id}/models/{model_name}	Update model by name in project
DELETE	/projects/{project_id}/models/{model_name}	Delete model by name in project
GET	/projects/{project_id}/models/{model_name}/related_models_count	Get related models count
PUT	/projects/{project_id}/models/{model_name}/fields/{field_key}/description	Edit model field description
GET	/projects/{project_id}/models/{model_name}/lookup	Lookup model data

Records

Method	Path	Summary
GET	/records	List all records
POST	/records	Create a new record
GET	/projects/{project_id}/models/{model_name}/records	List records for a model in a project
POST	/projects/{project_id}/models/{model_name}/records/upload	Upload records via TSV
GET	/projects/{project_id}/models/{model_name}/records/{record_id}	Get record by ID
PUT	/projects/{project_id}/models/{model_name}/records/{record_id}	Update record by ID
DELETE	/projects/{project_id}/models/{model_name}/records/{record_id}	Delete record by ID
GET	/projects/{project_id}/models/{model_name}/records/{record_id}/related_records	Get related records for a record

Links

Method	Path	Summary
GET	/links	List all links
POST	/links	Create a new link
GET	/projects/{project_id}/models/{model_name}/links	List links for a model in a project
GET	/projects/{project_id}/models/{model_name}/links/{type}/{name}	Get a specific link by type and name

---

OpenAPI Schemas

The SCIENTRY API follows the OpenAPI 3.0 specification. Below is the complete schema definition:

openapi: 3.0.0

info:
  version: "0.0.1"
  title: "LIMS API"
  contact:
    email: "emilio.righi@crg.eu"

tags:
- name: "projects"
- name: "links"
- name: "audit"
- name: "files"
- name: "models"
- name: "records"
- name: "stats"
- name: "users"
- name: "upload"

components:
  schemas:
    Project:
      type: "object"
      properties: 
        name:
          type: "string"
        description:
          type: "string"
        version:
          type: "string"
        archived:
          type: "boolean"
        created_by:
          type: "string"

    Model:
      type: "object"
      properties:
        name:
          type: "string"
        description:
          type: "string"
        reference_model:
          type: "string"
        project_id:
          type: "string"
        inherit_reference_id:
          type: "boolean"
        fields:
          type: "array"
          items:
            $ref: "#/components/schemas/Filter"

    Record:
      type: "object"
      properties:
        item_id:
          type: "string"
        model_name:
          type: "string"
        project_id:
          type: "string"
        reference_id:
          type: "string"
        created_by:
          type: "string"
      additionalProperties:
        oneOf:
          - type: "string"
          - type: "number"
          - type: "string"
            format: "date"
          - type: "array"
            items:
              type: "string"
      description: "Record object with dynamic attributes based on Filter schema. Additional properties can be added where the key is the Field name and the value matches the Field type."

    FileLink:
      type: "object"
      properties:
        name:
          type: "string"
        description:
          type: "string"
        type:
          type: "string"
          enum:
            - "images"
            - "protocols"
            - "analysis"
        created_by:
          type: "string"
        project_id:
          type: "string"
        model_name:
          type: "string"

    Filter:
      type: "object"
      properties:
        key:
          type: "string"
        required:
          type: "boolean"
        multi:
          type: "boolean"
        regex:
          type: "string"
        choices:
          type: "array"
          items:
            type: "string"
        description:
          type: "string"
        type:
          type: "string"
          enum:
            - "text"
            - "number"
            - "date"
            - "select"

Data Types

Field Types

The following field types are supported in SCIENTRY:

• text: String values
• number: Numeric values
• date: Date values (ISO 8601 format)
• select: Choice from predefined options

Record Dynamic Attributes

Records support dynamic attributes based on the Filter schema. Each additional property in a record must:

1. Have a key that corresponds to a Filter's key field
2. Have a value that matches the Filter's type field

Validation Rules

Required Fields

Fields marked as required: true must have values when creating or updating records.

Multi-Value Fields

Fields with multi: true can accept multiple values (arrays).

Regular Expression Validation

Fields with a regex pattern will validate input against that pattern.

Choice Validation

Fields of type select must have values that match one of the predefined choices.

Examples

Creating a Record with Dynamic Attributes

{
  "item_id": "SAMPLE_001",
  "model_name": "Biosamples",
  "project_id": "PROJ_001",
  "reference_id": "REF_001",
  "created_by": "user123",
  "sample_id": "SAMPLE_001",
  "collection_date": "2024-01-15",
  "temperature": 25.5,
  "location": "Lab A"
}

In this example:

• sample_id corresponds to a Filter with key: "sample_id" and type: "text"
• collection_date corresponds to a Filter with key: "collection_date" and type: "date"
• temperature corresponds to a Filter with key: "temperature" and type: "number"
• location corresponds to a Filter with key: "location" and type: "text"

API Endpoints

For complete API endpoint documentation, see the API Reference Overview.